Performance optimization for parallel processing on a multiple-CPU server

Symmetric multi-processor (SMP) systems, or multiple-CPU servers, are suitable for implementing parallel algorithms because they employ dedicated communication devices to enhance the inter-processor communication bandwidth, so that a better performance can be obtained. However, the cost for a multiple-CPU server is high and therefore, the server is usually shared among many users. The work-load due to other users will certainly affect the performance of the parallel programs so it is desirable to derive a method to optimize parallel programs under different loading conditions. In this paper, we present a simple method, which can be applied in SPMD type parallel programs, to improve the speedup by controlling the number of threads within the programs.

Parallel solution for railway power network simulation

The Streaming SIMD extension (SSE) is a special feature that is available in the Intel Pentium III and P4 classes of microprocessors. As its name implies, SSE enables the execution of SIMD (Single Instruction Multiple Data) operations upon 32-bit floating-point data therefore, performance of floating-point algorithms can be improved. In electrified railway system simulation, the computation involves the solving of a huge set of simultaneous linear equations, which represent the electrical characteristic of the railway network at a particular time-step and a fast solution for the equations is desirable in order to simulate the system in real-time. In this paper, we present how SSE is being applied to the railway network simulation.

Real-time simulation for power systems based on parallel computing - an empirical study

Abstract Computer simulation is a versatile and commonly used tool for the design and evaluation of systems with different degrees of complexity. Power distribution systems and electric railway network are areas for which computer simulations are being heavily applied. A dominant factor in evaluating the performance of a software simulator is its processing time, especially in the cases of real-time simulation. Parallel processing provides a viable mean to reduce the computing time and is therefore suitable for building real-time simulators. In this paper, we present different issues related to solving the power distribution system with parallel computing based on a multiple-CPU server and we will concentrate, in particular, on the speedup performance of such an approach.

Teaching parallel computing concepts with a desktop computer

Parallel computing is currently used in many engineering problems. However, because of limitations in curriculum design, it is not always possible to offer students specific formal teaching in this topic. Furthermore, parallel machines are still too expensive for many institutions. The latest microprocessors, such as Intel’s Pentium III and IV, embody single instruction multiple-data (SIMD) type parallel features, which makes them a viable solution for introducing parallel computing concepts to students. Final year projects have been initiated utilizing SSE (streaming SIMD extensions) features and it has been observed that students can easily learn parallel programming concepts after going through some programming exercises. They can now experiment with parallel algorithms on their own PCs at home. Keywords

Parallel user profiling based on folksonomy for Large Scaled Recommender Systems : an implimentation of Cascading MapReduce

The Large scaled emerging user created information in web 2.0 such as tags, reviews, comments and blogs can be used to profile users’ interests and preferences to make personalized recommendations. To solve the scalability problem of the current user profiling and recommender systems, this paper proposes a parallel user profiling approach and a scalable recommender system. The current advanced cloud computing techniques including Hadoop, MapReduce and Cascading are employed to implement the proposed approaches. The experiments were conducted on Amazon EC2 Elastic MapReduce and S3 with a real world large scaled dataset from Del.icio.us website.

Frequent activating FGFR2 mutations in endometrial carcinomas parallel germline mutations associated with craniosynostosis and skeletal dysplasia syndromes

Endometrial carcinoma is the most common gynecological malignancy in the United States. Although most women present with early disease confined to the uterus, the majority of persistent or recurrent tumors are refractory to current chemotherapies. We have identified a total of 11 different FGFR2 mutations in 3/10 (30%) of endometrial cell lines and 19/187 (10%) of primary uterine tumors. Mutations were seen primarily in tumors of the endometrioid histologic subtype (18/115 cases investigated, 16%). The majority of the somatic mutations identified were identical to germline activating mutations in FGFR2 and FGFR3 that cause Apert Syndrome, Beare-Stevenson Syndrome, hypochondroplasia, achondroplasia and SADDAN syndrome. The two most common somatic mutations identified were S252W (in eight tumors) and N550K (in five samples). Four novel mutations were identified, three of which are also likely to result in receptor gain-of-function. Extensive functional analyses have already been performed on many of these mutations, demonstrating they result in receptor activation through a variety of mechanisms. The discovery of activating FGFR2 mutations in endometrial carcinoma raises the possibility of employing anti-FGFR molecularly targeted therapies in patients with advanced or recurrent endometrial carcinoma.

Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant

Background Invasive species pose a significant threat to global economies, agriculture and biodiversity. Despite progress towards understanding the ecological factors associated with plant invasions, limited genomic resources have made it difficult to elucidate the evolutionary and genetic factors responsible for invasiveness. This study presents the first expressed sequence tag (EST) collection for Senecio madagascariensis, a globally invasive plant species. Methods We used pyrosequencing of one normalized and two subtractive libraries, derived from one native and one invasive population, to generate an EST collection. ESTs were assembled into contigs, annotated by BLAST comparison with the NCBI non-redundant protein database and assigned gene ontology (GO) terms from the Plant GO Slim ontologies. Key Results Assembly of the 221 746 sequence reads resulted in 12 442 contigs. Over 50 % (6183) of 12 442 contigs showed significant homology to proteins in the NCBI database, representing approx. 4800 independent transcripts. The molecular transducer GO term was significantly over-represented in the native (South African) subtractive library compared with the invasive (Australian) library. Based on NCBI BLAST hits and literature searches, 40 % of the molecular transducer genes identified in the South African subtractive library are likely to be involved in response to biotic stimuli, such as fungal, bacterial and viral pathogens. Conclusions This EST collection is the first representation of the S. madagascariensis transcriptome and provides an important resource for the discovery of candidate genes associated with plant invasiveness. The over-representation of molecular transducer genes associated with defence responses in the native subtractive library provides preliminary support for aspects of the enemy release and evolution of increased competitive ability hypotheses in this successful invasive. This study highlights the contribution of next-generation sequencing to better understanding the molecular mechanisms underlying ecological hypotheses that are important in successful plant invasions.

Parallel implementation of stochastic simulation for large scale cellular processes

Experimental and theoretical studies have shown the importance of stochastic processes in genetic regulatory networks and cellular processes. Cellular networks and genetic circuits often involve small numbers of key proteins such as transcriptional factors and signaling proteins. In recent years stochastic models have been used successfully for studying noise in biological pathways, and stochastic modelling of biological systems has become a very important research field in computational biology. One of the challenge problems in this field is the reduction of the huge computing time in stochastic simulations. Based on the system of the mitogen-activated protein kinase cascade that is activated by epidermal growth factor, this work give a parallel implementation by using OpenMP and parallelism across the simulation. Special attention is paid to the independence of the generated random numbers in parallel computing, that is a key criterion for the success of stochastic simulations. Numerical results indicate that parallel computers can be used as an efficient tool for simulating the dynamics of large-scale genetic regulatory networks and cellular processes

Microstrip to parallel strip balun as spiral antenna feed

This paper presents the design and implementation of a microstrip to parallel strip balun which are frequently used as balanced antennas feed. This wideband balun transition is composed of a parallel strip which is connected to the spiral antenna and a microstrip line where the width of the ground plane is gradually reduced to eventually resemble the parallel strip. The taper accomplishes the mode and impedance transformation. This balun has significantly improved bandwidth characteristics. The entire circuit was fabricated on RT Duriod 5880 substrate. The circuit designs were simulated and optimised using CST Microwave Studio and the simulated results are compared with the measured results. The back-to-back microstrip to parallel strip has a return loss of better than 10 dB over a wide bandwidth from 1.75 to 15 GHz. The performance of the proposed balun was validated with the spiral antenna. The measured results were compared with the simulated results and it shows that the antenna operates well in wideband frequency range from 2.5 to 15 GHz.

Scheduling Trains with Priorities : a no-wait blocking parallel-machine job-shop scheduling model

The paper investigates train scheduling problems when prioritised trains and non-prioritised trains are simultaneously traversed in a single-line rail network. In this case, no-wait conditions arise because the prioritised trains such as express passenger trains should traverse continuously without any interruption. In comparison, non-prioritised trains such as freight trains are allowed to enter the next section immediately if possible or to remain in a section until the next section on the routing becomes available, which is thought of as a relaxation of no-wait conditions. With thorough analysis of the structural properties of the No-Wait Blocking Parallel-Machine Job-Shop-Scheduling (NWBPMJSS) problem that is originated in this research, an innovative generic constructive algorithm (called NWBPMJSS_Liu-Kozan) is proposed to construct the feasible train timetable in terms of a given order of trains. In particular, the proposed NWBPMJSS_Liu-Kozan constructive algorithm comprises several recursively-used sub-algorithms (i.e. Best-Starting-Time-Determination Procedure, Blocking-Time-Determination Procedure, Conflict-Checking Procedure, Conflict-Eliminating Procedure, Tune-up Procedure and Fine-tune Procedure) to guarantee feasibility by satisfying the blocking, no-wait, deadlock-free and conflict-free constraints. A two-stage hybrid heuristic algorithm (NWBPMJSS_Liu-Kozan-BIH) is developed by combining the NWBPMJSS_Liu-Kozan constructive algorithm and the Best-Insertion-Heuristic (BIH) algorithm to find the preferable train schedule in an efficient and economical way. Extensive computational experiments show that the proposed methodology is promising because it can be applied as a standard and fundamental toolbox for identifying, analysing, modelling and solving real-world scheduling problems.